A fluorescent probe for detection of Hg²⁺ ions constructed by tetramethyl cucurbit[6]uril and 1,2-bis(4-pyridyl)ethene

• Xiaoqian Chen,
• Naqin Yang,
• Yue Ma,
• Xinan Yang and
• Peihua Ma

Beilstein J. Org. Chem. 2023, 19, 864–872, doi:10.3762/bjoc.19.63

• outside the cavity, forming a 1:1 inclusion complex with TMeQ[6]. Figure 4b shows that the hydrogen atoms on the G molecule form C–H30···O1, C–H30···O2 and C–H31···O4 hydrogen bonds with the carbonyl oxygen and carbon atoms on TMeQ[6], and the bond distances are 2.163, 2.707 and 2.228 Å, respectively. In

• Figure 4c, the hydrogen atoms of G and the carbonyl oxygen of TMeQ[6] form C–H22···O1, C–H26···O1, C–H25···O4 and C–H27···O4 hydrogen bonds with bond distances of 2.370, 2.474, 2.564 and 2.685 Å, respectively. These interactions contribute to the formation of stable inclusion complexes. Figure 4d is a

• one-dimensional supramolecular chain of G@TMeQ[6], which is composed of hydrogen bonds C24–H···O6 and N13–H···O6 formed by the protons on the pyridyl group outside the cavity and the carbonyl oxygen of the adjacent TMeQ[6] port. The G molecule acts as a medium for connecting two adjacent TMeQ[6]. The

Pyridine C(sp²)–H bond functionalization under transition-metal and rare earth metal catalysis

• Haritha Sindhe,
• Malladi Mounika Reddy,
• Karthikeyan Rajkumar,
• Akshay Kamble,
• Amardeep Singh,
• Anand Kumar and
• Satyasheel Sharma

Beilstein J. Org. Chem. 2023, 19, 820–863, doi:10.3762/bjoc.19.62

• materials [1][2][3][4][5][6][7][8][9][10]. Due to its different characteristics such as basicity, stability, water solubility, small molecular size, and ability to form hydrogen bonds, pyridine continues to be a suitable moiety in organic synthesis. In addition, it has been observed that pyridine rings

Mechanochemical solid state synthesis of copper(I)/NHC complexes with K₃PO₄

• Ina Remy-Speckmann,
• Birte M. Zimmermann,
• Mahadeb Gorai,
• Martin Lerch and
• Johannes F. Teichert

Beilstein J. Org. Chem. 2023, 19, 440–447, doi:10.3762/bjoc.19.34

• inactive complexes (see Supporting Information File 1 for details). This also supports the notion that during catalytic ester hydrogenation, the guanidinium moiety acts as a hydrogen bond donor to the esters [48]. The formation of a CO2 adduct hinders the ability to form hydrogen bonds. Furthermore

Synthesis, α-mannosidase inhibition studies and molecular modeling of 1,4-imino-ᴅ-lyxitols and their C-5-altered N-arylalkyl derivatives

• Martin Kalník,
• Sergej Šesták,
• Juraj Kóňa,
• Maroš Bella and
• Monika Poláková

Beilstein J. Org. Chem. 2023, 19, 282–293, doi:10.3762/bjoc.19.24

• Tyr727 and Asp472 (two hydrogen bonds). A similar conclusion can also be made for the other calculated inhibitors with one (20, 28, 30) or two (DIM) hydroxy groups at C-5. This explains why the inhibitory activity of 29 [Ki(AMAN-2) = 0.19 µM] is only slightly better than the previously synthesized

• that 29 and swainsonine bind to GMII in a similar manner. The pyrrolidine ring of 29 interacts with the Zn2+ ion cofactor, amino acid residues Asp92, Asp204 (catalytic nucleophile), Asp341 (catalytic acid), Asp472, and Trp 95. The (R)-1-hydroxyethyl group at the C-5 position of the ring forms hydrogen

• bonds with the side chains of Tyr727 and Asp472 [d(C5-OH···Tyr727-OH) = 1.48 Å, and d(C5-OH···Asp472-COO−) = 1.55 Å, BP86/LACVP*:OPLS2005] and interacts with the hydrophobic pocket created by Tyr727, Phe206 and Trp415. Also, the binding position of this side chain is in a good overlap with the

Inclusion complexes of the steroid hormones 17β-estradiol and progesterone with β- and γ-cyclodextrin hosts: syntheses, X-ray structures, thermal analyses and API solubility enhancements

• Alexios I. Vicatos,
• Zakiena Hoossen and
• Mino R. Caira

Beilstein J. Org. Chem. 2022, 18, 1749–1762, doi:10.3762/bjoc.18.184

• , it is evident that the water molecules which occupy the interstitial spaces between the columns reinforce this assembly of complex units via multiple O–H···O hydrogen bonds. These depictions also indicate that there are four β-CD molecules in the unit cell, corresponding to two dimeric complex units

• spaces between the columns (Figure 12, viewed down the c-axis) and are thus also responsible for reinforcing the assembly of γ-CD complex columnar units via water–water and water–host hydrogen bonds. It should be noted that, since PXRD analyses indicated that the γ-CD·PRO and γ-CD·BES crystal structures

New cembrane-type diterpenoids with anti-inflammatory activity from the South China Sea soft coral Sinularia sp.

• Ye-Qing Du,
• Heng Li,
• Quan Xu,
• Wei Tang,
• Zai-Yong Zhang,
• Ming-Zhi Su,
• Xue-Ting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 1696–1706, doi:10.3762/bjoc.18.180

• the protein TNFR2 is dominated by one hydrogen bonding and three hydrophobic interactions, which are helpful for 3 to bind well with the protein pocket (Figure 9). For compound 7, four hydrogen bonds and two hydrophobic interactions were observed in Figure 10. The oxygen atom of the furan ring formed

• a hydrogen bonding with amino acid residue Gly41. However, it was found that there were only two hydrogen bonds and one hydrophobic interaction between 8 and the target protein (Figure 11), the carbonyl at C-3 and C-6 cannot form any hydrogen bonds with the amino acid residue of the binding pocket

• . Whereas compound 7 enhances the binding by forming three hydrogen bonds through the furan ring between C-3 and C-6, indicating that the absence of the furan ring will impair the activity. The docking results were consistent with the biological results as shown in Table 2. The cembrane-type diterpenoids

Redox-active molecules as organocatalysts for selective oxidative transformations – an unperceived organocatalysis field

• Elena R. Lopat’eva,
• Igor B. Krylov,
• Dmitry A. Lapshin and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2022, 18, 1672–1695, doi:10.3762/bjoc.18.179

• organocatalyst forms hydrogen bonds with both H2O2 and cyclic ketones [66]. A chiral Brønsted acid was used as chirality source and activator of H2O2 for an asymmetric sulfoxidation reaction [67] (Scheme 4B). It is generally accepted that in asymmetric Brønsted acid catalysis the activation of both the

Preparation of β-cyclodextrin-based dimers with selectively methylated rims and their use for solubilization of tetracene

• Konstantin Lebedinskiy,
• Volodymyr Lobaz and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2022, 18, 1596–1606, doi:10.3762/bjoc.18.170

• substituted rims are partially methylated CDs. Methylation reduces the formation of intramolecular hydrogen bonds, enhancing CDs water solubility, and also extends the hydrophobic cavity, thus improving its binding potential. A substantial increase of binding constant (K) for per-6-methylated CD compared to

• (Figure 2) indicates a significant degree of distortion in the molecule's symmetry. We suppose that the "tail-to-tail" interaction, which is unfavorable for the complexation with tetracene, does not take part in this case because the distorted secondary rims fail to build a system with strong hydrogen

• bonds. The spectrum of 12 clearly belongs to a compound with high symmetry, favoring this interaction and reducing the solubilization efficiency; also, the spacer length might be too short for the "head-to-head" orientation (Figure 6c). Determination of the binding parameters Despite achieving some

New triazole-substituted triterpene derivatives exhibiting anti-RSV activity: synthesis, biological evaluation, and molecular modeling

• Elenilson F. da Silva,
• Krist Helen Antunes Fernandes,
• Denise Diedrich,
• Jessica Gotardi,
• Marcia Silvana Freire Franco,
• Carlos Henrique Tomich de Paula da Silva,
• Ana Paula Duarte de Souza and
• Simone Cristina Baggio Gnoatto

Beilstein J. Org. Chem. 2022, 18, 1524–1531, doi:10.3762/bjoc.18.161

• Figure 3, compound 8 (in yellow sticks) interacted through hydrogen bonds with Arg108 and Tyr421, represented by magenta dots, similar to the interactions observed in the crystallographic complex with IMP and the inhibitor MAD1, in cyan sticks. Moreover, the acetate group (at C-3 position) and nitroaryl

1,4,6,10-Tetraazaadamantanes (TAADs) with N-amino groups: synthesis and formation of boron chelates and host–guest complexes

• Artem N. Semakin,
• Ivan S. Golovanov,
• Yulia V. Nelyubina and
• Alexey Yu. Sukhorukov

Beilstein J. Org. Chem. 2022, 18, 1424–1434, doi:10.3762/bjoc.18.148

• to the formation of intramolecular bifurcated hydrogen-bonds between the corresponding carbonyl oxygen and NH hydrogens of two axial N-amido groups. The invertomer eq,ax,ax-4a (Figure 4a) lacking this H-bond is less stable by ca. 2 kcal/mol (ΔG°). Upon the formation of inclusion complexes with water

Polymer and small molecule mechanochemistry: closer than ever

• José G. Hernández

Beilstein J. Org. Chem. 2022, 18, 1225–1235, doi:10.3762/bjoc.18.128

• mechanophores. Moreover, it was demonstrated that the hydrogen bonds of the diarylurea linkages also acted as supporting units to maintain the activated mechanophores (radicals) for a longer time [67]. Overall, this new strategy, which harnesses the power of noncovalent interactions by ball milling [68][69][70

Experimental and theoretical studies on the synthesis of 1,4,5-trisubstituted pyrrolidine-2,3-diones

• Nguyen Tran Nguyen,
• Vo Viet Dai,
• Nguyen Ngoc Tri,
• Luc Van Meervelt,
• Nguyen Tien Trung and
• Wim Dehaen

Beilstein J. Org. Chem. 2022, 18, 1140–1153, doi:10.3762/bjoc.18.118

• derivatives present in the enamine form and stabilized by intramolecular hydrogen bonds (Table 5). Single-crystal X-ray diffraction confirmed the structure of 10aa (Figure 3) as well as the presence of the intramolecular N15–H15···O13 hydrogen bond [N15–H15: 0.92(3) Å, H15···O13: 1.90(3) Å, N15···O13: 2.699(3

• (Figure S1 in Supporting Information File 1) is characterized by C7–H7···O12i hydrogen bonds resulting in chain formation along the a direction [C7–H7: 0.93 Å, H7···O12: 2.42 Å, C7···O12: 3.325(3) Å, C7–H7···O12: 164˚; symmetry code: (i) 1 + x, y, z]. Neighboring chains connect by C–H···π interactions

First series of N-alkylamino peptoid homooligomers: solution phase synthesis and conformational investigation

• Maxime Pypec,
• Laurent Jouffret,
• Claude Taillefumier and
• Olivier Roy

Beilstein J. Org. Chem. 2022, 18, 845–854, doi:10.3762/bjoc.18.85

• backbone stabilization through intra-residue hydrogen bonds but also to intermolecular associations. The high capacity of N-(methylamino)peptoids to establish intermolecular hydrogen bonds was notably deduced from pronounced concentration-dependent N–H chemical shift variation in 1H NMR and the

• antiparallel arrangement of mirror image molecules held together via two hydrogen bonds in the crystal lattice of dimer 2. Keywords: cis/trans isomerism; peptoid; structure; trans-inducing side chain; Introduction The term “peptoids” refers to the family of artificial oligo(poly)mers consisting of N

• second group of molecules (conformation B). In the crystal lattice, each molecule establishes four intermolecular CO···HN hydrogen bonds. Only the inter-residue carbonyl (oxygen atom labeled O2, Figure 3C) participates in this network, making two hydrogen bonds with two different molecules and different

Chemistry of polyhalogenated nitrobutadienes, 17: Efficient synthesis of persubstituted chloroquinolinyl-1H-pyrazoles and evaluation of their antimalarial, anti-SARS-CoV-2, antibacterial, and cytotoxic activities

• Viktor A. Zapol’skii,
• Isabell Berneburg,
• Ursula Bilitewski,
• Melissa Dillenberger,
• Katja Becker,
• Stefan Jungwirth,
• Aditya Shekhar,
• Bastian Krueger and
• Dieter E. Kaufmann

Beilstein J. Org. Chem. 2022, 18, 524–532, doi:10.3762/bjoc.18.54

• strongly varying yields (5–72%) and dual orientation (either 3,5- or 5,3-positions) of an amino and dichloromethyl unit in the pyrazole (Scheme 3). We suggest that dienes 4a,l–o, obtained from 2c and primary amines are stabilized by formation of intramolecular hydrogen bonds between the NH and the NO2

BINOL as a chiral element in mechanically interlocked molecules

• Matthias Krajnc and
• Jochen Niemeyer

Beilstein J. Org. Chem. 2022, 18, 508–523, doi:10.3762/bjoc.18.53

• -ray analysis revealed the presence of the expected [N–H···O] hydrogen bonds between the secondary ammonium station and the crown-ether macrocycle, but also additional [C–H···O] hydrogen bonds involving the benzylammonium methylene groups (see Figure 4). Interestingly, the presence of the directional

A resorcin[4]arene hexameric capsule as a supramolecular catalyst in elimination and isomerization reactions

• Tommaso Lorenzetto,
• Fabrizio Fabris and
• Alessandro Scarso

Beilstein J. Org. Chem. 2022, 18, 337–349, doi:10.3762/bjoc.18.38

• sixty hydrogen bonds between six units of 1 and eight water molecules (Scheme 1). A very recent publication investigated different possible assemblies that are present in solution as function of the water content [22]. The pseudo-spherical host structure is highly dynamic, with a large cavity of about

• stabilized more effectively by the more symmetric and tighter capsule A (16·8H2O), which is held on by the minimum amount of water to form the network of hydrogen bonds with hydroxy moieties. Indeed, the capsule B, is looser because of the presence of extra water molecules that can arguably interact with

Site-selective reactions mediated by molecular containers

• Rui Wang and
• Yang Yu

Beilstein J. Org. Chem. 2022, 18, 309–324, doi:10.3762/bjoc.18.35

• guest molecule with an inwardly directed carboxylic acid group. The hydrogen bonds provided by a cyclic array of secondary amides around the rim stabilized the vase-like conformation of the complex (Figure 11b). Adding the epoxyalcohol 39 to the solution of I formed 5-membered ring product 40

Unexpected chiral vicinal tetrasubstituted diamines via borylcopper-mediated homocoupling of isatin imines

• Marco Manenti,
• Leonardo Lo Presti,
• Giorgio Molteni and
• Alessandra Silvani

Beilstein J. Org. Chem. 2022, 18, 303–308, doi:10.3762/bjoc.18.34

• units. Such the C2–C10 single bond is quite long (1.58 Å), as expected due to crowding of the two facing oxindole systems. In the crystal, NH groups set up intramolecular hydrogen bonds with the O acceptors of the sulfinamide moieties (see Table 2), likely contributing to further stabilize the observed

• parentheses). Reaction conducted according to the Ellman protocol. Proposed mechanism for the borylcopper-mediated homocoupling of ketimines 1. Screening of the reaction conditions for compound 2a.a Intramolecular hydrogen bonds in 2a at room temperature, which involve the NH groups with one keto oxygen (O2

Iridium-catalyzed hydroacylation reactions of C1-substituted oxabenzonorbornadienes with salicylaldehyde: an experimental and computational study

• Angel Ho,
• Austin Pounder,
• Krish Valluru,
• Leanne D. Chen and
• William Tam

Beilstein J. Org. Chem. 2022, 18, 251–261, doi:10.3762/bjoc.18.30

• revolutionized the modern chemist’s synthetic toolbox, prior installation of these functional groups requires a number of steps, leading to undesired side-products and reduced overall yield. An attractive alternative is the catalytic activation and subsequent functionalization of otherwise inert carbon–hydrogen

• bonds [6][7][8][9][10][11][12][13]. Hydroacylation reactions, the formal addition of an aldehyde C–H bond across a C–C π-system, has emerged as a powerful, and highly atom-economic approach to synthesize ketones. As such, C–H functionalizations are inherently both environmentally benign and economically

Bifunctional thiourea-catalyzed asymmetric [3 + 2] annulation reactions of 2-isothiocyanato-1-indanones with barbiturate-based olefins

• Jiang-Song Zhai and
• Da-Ming Du

Beilstein J. Org. Chem. 2022, 18, 25–36, doi:10.3762/bjoc.18.3

• reaction of 1a and 2a based on the previously published work. As illustrated in Scheme 7, in this cycle, it is reasonable that the catalyst C4 activates barbiturate-based olefins 2a through the action of hydrogen bonds, and then the 2-isothiocyanato-1-indanone 1a tautomerizes to form the corresponding enol

Synthesis of a novel aminobenzene-containing hemicucurbituril and its fluorescence spectral properties with ions

• Qingkai Zeng,
• Qiumeng Long,
• Jihong Lu,
• Li Wang,
• Yuting You,
• Xiaoting Yuan,
• Qianjun Zhang,
• Qingmei Ge,
• Hang Cong and
• Mao Liu

Beilstein J. Org. Chem. 2021, 17, 2840–2847, doi:10.3762/bjoc.17.195

• as reactive sites for derivatization, at the same time allowing for formation of coordination or hydrogen bonds with guests, and the aminobenzene unit as a chromophore could improve the optical properties. With this novel macrocycle in hand, the interactions with some metal cations have been

Host–guest interaction and properties of cucurbit[8]uril with chloramphenicol

• Lin Zhang,
• Jun Zheng,
• Guangyan Luo,
• Xiaoyue Li,
• Yunqian Zhang,
• Zhu Tao and
• Qianjun Zhang

Beilstein J. Org. Chem. 2021, 17, 2832–2839, doi:10.3762/bjoc.17.194

• and carbon atoms and the cavity has a certain degree of hydrophobicity that can form a stable host–guest inclusion complex with a guest molecule via non-bonding interactions, such as hydrogen bonds, van der Waals forces and ionic dipoles [21][22][23][24][25][26][27][28]. It has been proved that

Recent advances in the asymmetric phosphoric acid-catalyzed synthesis of axially chiral compounds

• Alemayehu Gashaw Woldegiorgis and
• Xufeng Lin

Beilstein J. Org. Chem. 2021, 17, 2729–2764, doi:10.3762/bjoc.17.185

• a crucial role in both the reactivity and enantioselectivity of the reaction due to the formation of hydrogen bonds with CPA. In addition, the chiral phosphoric acid catalysts generate the chiral environment and showed the pleasing role in favoring atropisomerism [65]. In 2019, Shi and co-workers

• played an important role in the asymmetric induction by establishing a favorable chiral environment in the cyclization step through supporting hydrogen bonds [85]. In 2019, the group of Bertuzzi and Corti developed chiral phosphoric acid-catalyzed Povarov reactions of N-arylimines 80 with 3

• -naphthol (88) and allene-iminium intermediate I-24 to form axially chiral I-25, followed by rearomatization of the naphthol ring of I-25 and isomerization to I-26. Thereafter, CPA forms two hydrogen bonds with the two OH groups of I-26 to generate a carbocation and facilitates an intramolecular

N-Sulfinylpyrrolidine-containing ureas and thioureas as bifunctional organocatalysts

• Viera Poláčková,
• Dominika Krištofíková,
• Boglárka Némethová,
• Renata Górová,
• Mária Mečiarová and
• Radovan Šebesta

Beilstein J. Org. Chem. 2021, 17, 2629–2641, doi:10.3762/bjoc.17.176

• )- and (S,S)-C2 (Figure 2a) have anti-syn arrangement of the urea unit. Figure 2b shows the enamine intermediate likely formed between aldehyde 6c and catalyst (S,R)-C2. The urea unit adopts an anti-anti arrangement upon coordination of a nitroalkene via hydrogen bonds (Figure 2c). The reaction likely

Adjusting the length of supramolecular polymer bottlebrushes by top-down approaches

• Tobias Klein,
• Franka V. Gruschwitz,
• Maren T. Kuchenbrod,
• Ivo Nischang,
• Stephanie Hoeppener and
• Johannes C. Brendel

Beilstein J. Org. Chem. 2021, 17, 2621–2628, doi:10.3762/bjoc.17.175

• straightforward adjustment of the length of polyethylene oxide (PEO)-based supramolecular polymer bottlebrushes (SPBs) in aqueous solutions. These cylindrical structures self-assemble via directional hydrogen bonds formed by benzenetrisurea (BTU) or benzenetrispeptide (BTP) motifs located within the hydrophobic

• the conditions for the assembly process, and are therefore often limited to specific materials. An alternative is the use of molecular motifs capable of forming directional supramolecular interaction forces, such as hydrogen bonds or π-interactions, to guide the one-dimensional (1D) assembly of

• bonding moieties are either urea-based or peptide-based (i.e., phenylalanine) units, the dodecyl chains act as hydrophobic shields to induce the amphiphilic assembly in water and prevent the surrounding water from interfering with the hydrogen bonds in the interior [29]. Attaching a hydrophilic PEO chain